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Publication
Featured researches published by Alexander Nagy.
Virus Research | 2012
Alexander Nagy; Lenka Černíková; Vlastimil Křivda; Jitka Horníčková
The objective of our study was to provide a genotype analysis of H7N7 and H7N9 influenza A viruses (IAV) and infer their relationships to co-circulating non-H7 IAV genomes. The H7N7 strains were collected in central Europe (Hungary-1, Czech Republic-1, Slovenia-1 and Poland-4) and the H7N9 in the Czech Republic and Spain between 2007 and 2011. Hand in hand with this effort, a novel IAV genotype visualization approach called digital genotyping was developed. This approach relies on phylogenetic data summarization and transformation into a pixel array called a segment identity matrix. The digital genotyping revealed a complicated genetic interplay between the H7 and co-circulating non-H7 IAV genotypes. At the H7 IAV level the most obvious relationships were observed between one Polish H7N7/446/09 and Czech H7N7/11 viruses which, despite the special and temporal distance of 800 km and 15 months, retained at least 6/8 genome segments. Close relationships were also observed between the Czech H7N9, Polish and Slovenian H7N7 on one hand and Hungarian and Slovenian H7N7 isolates on the other. In addition the former genomes exhibited close interplays with the Czech H6N2/09 and H11N9/10-like viruses. The Czech and Spanish H7N9 genomes were completely different and 6/8 of the Czech H7N9-like segments were traced to either the Czech H3N8/07, H11N9/09 and Polish H7N7/09-like viruses. The results of digital genotyping correlated with the previous observations obtained on the Polish H7N7 isolates. As was demonstrated, the digital genotyping provides a well-arranged and easily interpretable output and may serve as an alternative genotyping tool useful for handling and analysing even a large panel of IAV genomes.
Archives of Virology | 2010
Alexander Nagy; Veronika Vostinakova; Zuzana Pirchanova; Lenka Černíková; Zuzana Dirbakova; Miroslav Mojzis; Helena Jirincova; Martina Havlíčková; Ádám Dán; Krisztina Ursu; Stefan Vilcek; Jitka Horníčková
The objective of our study was to develop and evaluate a TaqMan real-time RT-PCR (RRT-PCR) assay for universal detection of influenza A (IA) viruses. The primers and LNA-modified octanucleotide probe were selected to correspond to extremely conserved regions of the membrane protein (MP) segment identified by a comprehensive bioinformatics analysis including 10,405 IA viruses MP sequences, i.e., all of the sequences of the Influenza Virus Sequence database collected as of August 20, 2009. The RRT-PCR has a detection limit of approximately five copies of target RNA/reaction and excellent reaction parameters tested in four IA viruses reference laboratories. The inclusivity of the assay was estimated at both the bioinformatic and the experimental level. Our results predicted that this RRT-PCR assay was able to detect 99.5% of known human IA virus strains, 99.84% of pandemic influenza A (H1N1) strains, 99.75% of avian strains, 98.89% of swine strains, 98.15% of equine strains, and 100% of influenza A viruses of other origin.
PLOS ONE | 2016
Alexander Nagy; Lenka Černíková; Eliška Vitásková; Vlastimil Křivda; Ádám Dán; Zuzana Dirbakova; Helena Jiřincová; Bohumír Procházka; Kamil Sedlák; Martina Havlíčková
In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence.
Veterinary Record | 2006
Ivan Holko; Jirina Machova; Jitka Horníčková; Miroslav Tomci; Ivan Nagl; Bedrich Horyna; Alexander Nagy
SIR, – Annual serological monitoring for avian influenza in wild birds and domestic poultry had been carried out in the Czech Republic without any case being reported until 2005. Following events regarding bird flu in Europe, an extensive surveillance study was carried out between January and
Methods of Molecular Biology | 2015
Alexander Nagy; Tomáš Jiřinec; Lenka Černíková; Helena Jiřincová; Martina Havlíčková
The development of a diagnostic polymerase chain reaction (PCR) or quantitative PCR (qPCR) assay for universal detection of highly variable viral genomes is always a difficult task. The purpose of this chapter is to provide a guideline on how to align, process, and evaluate a huge set of homologous nucleotide sequences in order to reveal the evolutionarily most conserved positions suitable for universal qPCR primer and hybridization probe design. Attention is paid to the quantification and clear graphical visualization of the sequence variability at each position of the alignment. In addition, specific problems related to the processing of the extremely large sequence pool are highlighted. All of these steps are performed using an ordinary desktop computer without the need for extensive mathematical or computational skills.
PLOS ONE | 2014
Alexander Nagy; Lenka Černíková; Helena Jiřincová; Martina Havlíčková; Jitka Horníčková
Influenza A virus (IAV) in wild bird reservoir hosts is characterized by the perpetuation in a plethora of subtype and genotype constellations. Multiyear monitoring studies carried out during the last two decades worldwide have provided a large body of knowledge regarding the ecology of IAV in wild birds. Nevertheless, other issues of avian IAV evolution have not been fully elucidated, such as the complexity and dynamics of genetic interactions between the co-circulating IAV genomes taking place at a local-scale level or the phenomenon of frozen evolution. We investigated the IAV diversity in a mallard population residing in a single pond in the Czech Republic. Despite the relative small number of samples collected, remarkable heterogeneity was revealed with four different IAV subtype combinations, H6N2, H6N9, H11N2, and H11N9, and six genomic constellations in co-circulation. Moreover, the H6, H11, and N2 segments belonged to two distinguishable sub-lineages. A reconstruction of the pattern of genetic reassortment revealed direct parent-progeny relationships between the H6N2, H11N9 and H6N9 viruses. Interestingly the IAV, with the H6N9 subtype, was re-detected a year later in a genetically unchanged form in the close proximity of the original sampling locality. The almost absolute nucleotide sequence identity of all the respective genomic segments between the two H6N9 viruses indicates frozen evolution as a result of prolonged conservation in the environment. The persistence of the H6N9 IAV in various abiotic and biotic environmental components was also discussed.
Archives of Virology | 2018
Alexander Nagy; Ádám Dán; Lenka Černíková; Eliška Vitásková; Vlastimil Křivda; Jitka Horníčková; Roman Masopust; Kamil Sedlák
Here, we present a comprehensive analysis of the H5N8/H5N5 highly pathogenic avian influenza (HPAI) virus strains detected in the Czech Republic during an outbreak in 2017. Network analysis of the H5 Hemagglutinin (HA) from 99% of the outbreak localities suggested that the diversity of the Czech H5N8/H5N5 viruses was influenced by two basic forces: local microevolution and independent incursions. The geographical occurrence of the central node H5 HA sequences revealed three eco-regions, which apparently played an important role in the origin and further spread of the local H5N8/HPAI variants across the country. A plausible explanation for the observed pattern of diversity is also provided.
Scientific Reports | 2017
Alexander Nagy; Eliška Vitásková; Lenka Černíková; Vlastimil Křivda; Helena Jiřincová; Kamil Sedlák; Jitka Horníčková; Martina Havlíčková
Ongoing evolution of viral pathogens is a significant issue in diagnostic virology employing TaqMan qPCR/RT-qPCR. Specific concerns are related to false negativity due to probe binding failure. One option for compensating for such deficiency is to integrate a second identically labelled probe in the assay. However, how this alteration influences the reaction parameters has not been comprehensively demonstrated. In the present study, we evaluate a TaqMan protocol using two identically labelled hydrolysis probes (simple, LNA (locked-nucleic-acid)) and MGB (minor-groove-binder) modified probes and combinations thereof in a single assay. Our results based on a synthetic amplicon suggest that the second probe does not compromise the TaqMan qPCR/RT-qPCR parameters, which repeatedly and reproducibly remained comparable to those of the corresponding single-probe assays, irrespective of the relative probe orientation, whether opposite or tandem, and probe modifications or combinations thereof. On the other hand, the second probe additively contributed to the overall fluorescence signal. The utility of the dual-probe approach was demonstrated on practical examples by using field specimens. We hope that the present study might serve as a theoretical basis for the development or improvement of TaqMan qPCR/RT-qPCR assays for the detection of highly variable nucleic acid templates.
Journal of Virological Methods | 2017
Lenka Černíková; Eliška Vitásková; Alexander Nagy
Psittacine beak and feather disease (PBFD) is one of the most significant viral diseases in psittacine birds. The aim of the presented study was to develop a highly specific and sensitive TaqMan real-time PCR assay for universal detection of beak and feather disease virus (BFDV). Primers and a hydrolysis probe were selected on the highly conserved regions belonging to the ORF1 of the BFDV genome which were identified by aligning 814 genomic sequences downloaded from the GenBank database. The evaluation of the reaction parameters suggested a reaction efficiency of 97.1%, with consistent detection of 101 virus copies/μl of nucleic acid extract. The low values of standard deviation and coefficient of variation indicate a high degree of reproducibility and repeatability. The diagnostic applicability of the assay was proven on 36 BFDV positive and 107 negative specimens of psittacine origin representing 28 species. The assay showed a 100% ability to detect distinct genetic variants of the virus. Our data suggest that the presented TaqMan real-time PCR represents a specific, sensitive and reliable assay facilitating the molecular detection of BFDV.
Veterinary Microbiology | 2007
Alexander Nagy; Jirina Machova; Jitka Horníčková; Miroslav Tomci; Ivan Nagl; Bedrich Horyna; Ivan Holko
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University of Veterinary and Pharmaceutical Sciences Brno
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